Fixing large fluctuations in pressure due to insufficient sampling in atomistic simulations?

Hello all, I was reading a paper on steered molecular dynamic (SMD). Then I realized the authors had to convert the system from all-atom to the coarse-grained configuration by using MARTINI force...

31 December 2017 7,393 0 View

Bad FENE bond error and fix nvt, fix nve problem in LAMPPS?

Hello everyone, I have a polymer with bond_style FENE every time that I comment the fix lines( except fix langevan) it works but as you know does not update the positions and if I uncomment the...

06 July 2016 6,893 1 View

United atom and all atom force field difference??

Hello everyone. I didn't understand difference between united atom and all atom force field. Is it just about Hydrogen and Carbon atoms?? Thanks.

03 April 2016 3,733 4 View

Problem with velocity polymer create command in LAMMPS?

02 March 2016 2,689 3 View

MD simulation in LAMMPS or GROMACS?

Hello everyone, I'm working on "Polymer translocation" and every time I search in internet, other researchers are talking about GROMACS. Is there a big problem with LAMMPS? Is GROMACS so easier...

02 March 2016 3,570 11 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View